Here is an update on what whiskies can be found in Japan (as of July 31st 2016). I have just returned from travelling Japan for three weeks and checked availabilities on countless occasions, including distilleries (both Yamazaki and Nikka), specialist shops, department stores, liquor stores and others. I will list whiskies based on how rare they are to find and add prices where it matters.
EASY TO FIND
There is a bunch of NAS whiskies that can be found in ordinary convenience stores. Each convenience store normally has a small selection of 20 cl bottles and a few 70 cl bottles. Check out a few of them and you should find all the following:
Nikka Miyagikyo (NAS)
Nikka Yoichi (NAS)
Nikka Taketsuru Pure Malt (NAS)
Suntory Hakushu (NAS)
Suntory Yamazaki (NAS)
Prices for 20 cl bottles vary between 1,000 and 1,400 yen. Nikka Coffey Malt and Nikka Coffey Grain are easy to find in department stores and liquor stores. No whiskies with an age-statement pop up in this category, unless you are interested in Nikka 12yr blended malt.
POSSIBLE TO FIND
If you are after the well-known brands with an age-statement, you could be lucky to find the following:
Suntory Hakushu 12yr (both as miniature and 70 cl bottle)
Suntory Yamazaki 12yr (mainly as 5 cl miniature)
Suntory Hibiki Japanese Harmony (NAS)
Suntory Hibiki 17yr (both as miniature and 70 cl bottle)
Hakushu 12 tends to be easier to find than Yamazaki 12, especially if you want to buy a 70 cl bottle (8,000-11,000 yen). 5 cl miniatures are an alternative (700-850 yen). Hibiki (NAS) costs about 5,000 yen and Hibiki 17yr between 11,000 and 17,000 yen (20,000 yen at Narita airport). 5 cl bottles of Hibiki 17 can be found for 800 yen. Focus on big department stores such as Bic Camera and others. Common liquor stores sometimes have one or two of the whiskies listed above.
HARD TO FIND
Now it becomes either difficult or expensive - or both. Liquors Hasegawa near Tokyo station (go to Yaesu central underground exit and proceed to the end of the T-shaped shopping area) is the first option here, but it is expensive!
Nikka Taketsuru 17yr
Suntory Hakushu 18yr
Suntory Yamazaki 12yr
Suntory Yamazaki 18yr
Suntory Hibiki 12yr (discontinued)
Liquors Hasegawa offered Yamazaki 12yr for 11,000 yen a bottle and Hakushu 18yr/Yamazaki 18yr for 45,800 yen a bottle. Some department stores have Yamazaki 12 for about 9,000 yen but in most places it is sold out. The discontinued Hibiki 12yr is difficult to find: I got 1 bottle from a liquor store in Abashiri (dusted shelves, last bottle) and to my surprise, there were some 50 cl bottles at Yamazaki distillery for sale. Not for long, I guess. Taketsuru 17 I saw twice, once in a department store near Shinjuku station and once in a liquor store in Hakodate. It costs between 7,000 and 8,000 yen.
Narita duty free is NOT the place to buy your whisky, the prices are for people who have more money than sense (50,000 yen for Hakushu 18yr/Yamazaki 18yr/Hibiki 21yr).
I got one bottle of Yamazaki 18yr at Yamazaki distillery but they sell it under the counter. If you do a tasting on 1st floor, be nice to the person in charge, taste the Yamazaki 18 and ask if you could buy a bottle. They make a phone call to the shop in 2nd floor and there you can get the bottle for 27,000 yen. Not sure if this works all the time, or if I was just lucky. They also have the 12yr under the counter.
IMPOSSIBLE TO FIND
Good luck to you if you are trying to find the following:
Nikka Miyagikyo 12yr
Nikka Yoichi 10yr / 12yr / 15 yr
Nikka Taketsuru 21yr
Suntory Yamazaki 25yr
All Nikka whiskies with an age-statement were discontinued in 2015 (except for Taketsuru 17 and 21) and I did not find a single bottle of them. Yamazaki 25 was sold out, even at Narita airport where it costs insane 250,000 yen.
Bottom line, if you are after a solid Japanese Single Malt with an age-statement, try to find a Yamazaki 12yr. In my opinion, the 18yr expression is only slightly better than its 6 years younger brother. Yamazaki 12 is an excellent choice, probably with the best price-quality ratio. However, the NAS Yamazaki is lacking cask influence and complexity.
Good luck to you! I hope that this was useful.